I had this question after viewing Missing Categories and colors in Outlook & Outlook.com
I was reviewing the above article because it is similar in nature to a event that a customer of mine is experiencing.
Outlook 2016, Office 365, Categories got reset to different colors and some were deselected from being shown.
I ran outlook.exe /remigratecategories.
That worked to bring them back, but the colors were wrong and certain categories were not selected any more to be shown.
Does anyone know what causes Office 365 / Outlook 2016 to lose these? Was it a update I ran? was it corruption of some sort?